Starting phenix.real_space_refine on Sat Aug 23 08:44:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xng_38503/08_2025/8xng_38503.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xng_38503/08_2025/8xng_38503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xng_38503/08_2025/8xng_38503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xng_38503/08_2025/8xng_38503.map" model { file = "/net/cci-nas-00/data/ceres_data/8xng_38503/08_2025/8xng_38503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xng_38503/08_2025/8xng_38503.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7240 2.51 5 N 1774 2.21 5 O 1858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10922 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5461 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 36, 'TRANS': 646} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Restraints were copied for chains: B Time building chain proxies: 3.64, per 1000 atoms: 0.33 Number of scatterers: 10922 At special positions: 0 Unit cell: (89.675, 140.315, 108.665, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1858 8.00 N 1774 7.00 C 7240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 399.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 2 sheets defined 72.5% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 removed outlier: 3.699A pdb=" N ILE A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.836A pdb=" N TYR A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.863A pdb=" N GLU A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 92 through 120 removed outlier: 4.536A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 121 through 124 removed outlier: 3.721A pdb=" N ASN A 124 " --> pdb=" O VAL A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 155 through 195 Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 242 through 269 Processing helix chain 'A' and resid 290 through 314 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 389 Processing helix chain 'A' and resid 389 through 398 removed outlier: 3.510A pdb=" N ILE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 420 through 437 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 456 through 475 Processing helix chain 'A' and resid 477 through 488 removed outlier: 3.907A pdb=" N GLU A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 494 removed outlier: 4.406A pdb=" N SER A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 508 through 523 removed outlier: 3.651A pdb=" N LYS A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 534 through 547 removed outlier: 3.611A pdb=" N LEU A 538 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 565 through 583 Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 590 through 612 removed outlier: 3.569A pdb=" N ILE A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 647 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 659 through 677 removed outlier: 4.031A pdb=" N VAL A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 684 through 699 removed outlier: 3.982A pdb=" N ALA A 688 " --> pdb=" O PRO A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 710 removed outlier: 4.162A pdb=" N ASN A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 31 removed outlier: 3.586A pdb=" N GLN B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.836A pdb=" N TYR B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.861A pdb=" N GLU B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 80 " --> pdb=" O MET B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 92 through 120 removed outlier: 4.535A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 121 through 124 removed outlier: 3.720A pdb=" N ASN B 124 " --> pdb=" O VAL B 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 124' Processing helix chain 'B' and resid 155 through 195 Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 242 through 269 Processing helix chain 'B' and resid 290 through 314 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 389 Processing helix chain 'B' and resid 389 through 398 removed outlier: 3.510A pdb=" N ILE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 420 through 437 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 477 through 488 removed outlier: 3.907A pdb=" N GLU B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 494 removed outlier: 4.406A pdb=" N SER B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 507 Processing helix chain 'B' and resid 508 through 523 removed outlier: 3.651A pdb=" N LYS B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 534 through 547 removed outlier: 3.611A pdb=" N LEU B 538 " --> pdb=" O MET B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 559 Processing helix chain 'B' and resid 565 through 583 Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 590 through 612 removed outlier: 3.569A pdb=" N ILE B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 647 Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 659 through 677 removed outlier: 4.031A pdb=" N VAL B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 684 through 699 removed outlier: 3.982A pdb=" N ALA B 688 " --> pdb=" O PRO B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 710 removed outlier: 4.162A pdb=" N ASN B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 238 removed outlier: 3.628A pdb=" N ALA A 323 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 206 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 238 removed outlier: 3.629A pdb=" N ALA B 323 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 206 " --> pdb=" O ALA B 323 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3302 1.34 - 1.45: 1831 1.45 - 1.57: 6001 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 11226 Sorted by residual: bond pdb=" CB TRP A 348 " pdb=" CG TRP A 348 " ideal model delta sigma weight residual 1.498 1.424 0.074 3.10e-02 1.04e+03 5.67e+00 bond pdb=" CB TRP B 348 " pdb=" CG TRP B 348 " ideal model delta sigma weight residual 1.498 1.424 0.074 3.10e-02 1.04e+03 5.66e+00 bond pdb=" CA GLU B 618 " pdb=" CB GLU B 618 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.46e-02 4.69e+03 3.79e+00 bond pdb=" CA GLU A 618 " pdb=" CB GLU A 618 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.46e-02 4.69e+03 3.72e+00 bond pdb=" CG1 ILE A 108 " pdb=" CD1 ILE A 108 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.02e+00 ... (remaining 11221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 14628 1.96 - 3.92: 528 3.92 - 5.89: 87 5.89 - 7.85: 17 7.85 - 9.81: 6 Bond angle restraints: 15266 Sorted by residual: angle pdb=" C ALA B 133 " pdb=" N LYS B 134 " pdb=" CA LYS B 134 " ideal model delta sigma weight residual 122.23 127.88 -5.65 1.48e+00 4.57e-01 1.46e+01 angle pdb=" C ALA A 133 " pdb=" N LYS A 134 " pdb=" CA LYS A 134 " ideal model delta sigma weight residual 122.23 127.83 -5.60 1.48e+00 4.57e-01 1.43e+01 angle pdb=" C ALA A 118 " pdb=" N VAL A 119 " pdb=" CA VAL A 119 " ideal model delta sigma weight residual 122.66 119.22 3.44 9.70e-01 1.06e+00 1.26e+01 angle pdb=" C ALA B 118 " pdb=" N VAL B 119 " pdb=" CA VAL B 119 " ideal model delta sigma weight residual 122.66 119.27 3.39 9.70e-01 1.06e+00 1.22e+01 angle pdb=" N PHE A 420 " pdb=" CA PHE A 420 " pdb=" C PHE A 420 " ideal model delta sigma weight residual 113.18 108.75 4.43 1.33e+00 5.65e-01 1.11e+01 ... (remaining 15261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 5915 17.28 - 34.56: 585 34.56 - 51.85: 94 51.85 - 69.13: 10 69.13 - 86.41: 16 Dihedral angle restraints: 6620 sinusoidal: 2584 harmonic: 4036 Sorted by residual: dihedral pdb=" CA ILE A 152 " pdb=" C ILE A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta harmonic sigma weight residual -180.00 -141.32 -38.68 0 5.00e+00 4.00e-02 5.98e+01 dihedral pdb=" CA ILE B 152 " pdb=" C ILE B 152 " pdb=" N PRO B 153 " pdb=" CA PRO B 153 " ideal model delta harmonic sigma weight residual -180.00 -141.35 -38.65 0 5.00e+00 4.00e-02 5.97e+01 dihedral pdb=" CA ASN A 475 " pdb=" C ASN A 475 " pdb=" N VAL A 476 " pdb=" CA VAL A 476 " ideal model delta harmonic sigma weight residual -180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 6617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1131 0.046 - 0.092: 447 0.092 - 0.137: 135 0.137 - 0.183: 11 0.183 - 0.229: 6 Chirality restraints: 1730 Sorted by residual: chirality pdb=" CB VAL A 476 " pdb=" CA VAL A 476 " pdb=" CG1 VAL A 476 " pdb=" CG2 VAL A 476 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL B 476 " pdb=" CA VAL B 476 " pdb=" CG1 VAL B 476 " pdb=" CG2 VAL B 476 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU A 579 " pdb=" CB LEU A 579 " pdb=" CD1 LEU A 579 " pdb=" CD2 LEU A 579 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1727 not shown) Planarity restraints: 1900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 348 " -0.037 2.00e-02 2.50e+03 3.73e-02 3.47e+01 pdb=" CG TRP A 348 " 0.095 2.00e-02 2.50e+03 pdb=" CD1 TRP A 348 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TRP A 348 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 348 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 348 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 348 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 348 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 348 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 348 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 348 " 0.037 2.00e-02 2.50e+03 3.72e-02 3.46e+01 pdb=" CG TRP B 348 " -0.095 2.00e-02 2.50e+03 pdb=" CD1 TRP B 348 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TRP B 348 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 348 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 348 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 348 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 348 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 348 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 348 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 31 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO B 32 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.038 5.00e-02 4.00e+02 ... (remaining 1897 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 359 2.70 - 3.25: 12431 3.25 - 3.80: 18229 3.80 - 4.35: 21566 4.35 - 4.90: 35605 Nonbonded interactions: 88190 Sorted by model distance: nonbonded pdb=" O LYS B 303 " pdb=" OG SER B 306 " model vdw 2.146 3.040 nonbonded pdb=" O LYS A 303 " pdb=" OG SER A 306 " model vdw 2.146 3.040 nonbonded pdb=" O GLN A 135 " pdb=" ND2 ASN A 138 " model vdw 2.189 3.120 nonbonded pdb=" O GLN B 135 " pdb=" ND2 ASN B 138 " model vdw 2.189 3.120 nonbonded pdb=" O PHE B 454 " pdb=" OG1 THR B 455 " model vdw 2.194 3.040 ... (remaining 88185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.580 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 11226 Z= 0.334 Angle : 0.892 9.810 15266 Z= 0.484 Chirality : 0.052 0.229 1730 Planarity : 0.006 0.069 1900 Dihedral : 14.281 86.411 3996 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.22), residues: 1350 helix: 0.08 (0.16), residues: 894 sheet: -2.64 (0.82), residues: 46 loop : -3.39 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 682 TYR 0.030 0.003 TYR B 468 PHE 0.037 0.002 PHE B 224 TRP 0.095 0.004 TRP A 348 HIS 0.005 0.001 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00759 (11226) covalent geometry : angle 0.89191 (15266) hydrogen bonds : bond 0.12054 ( 682) hydrogen bonds : angle 5.44320 ( 2016) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.6373 (mtt180) cc_final: 0.4964 (mtt90) REVERT: A 180 GLU cc_start: 0.7247 (tp30) cc_final: 0.6926 (tp30) REVERT: A 260 ASP cc_start: 0.8798 (m-30) cc_final: 0.8583 (m-30) REVERT: A 303 LYS cc_start: 0.8397 (ptpp) cc_final: 0.8075 (ptmt) REVERT: A 448 MET cc_start: 0.7717 (ttm) cc_final: 0.7340 (ttm) REVERT: A 521 MET cc_start: 0.8320 (tpp) cc_final: 0.8096 (mmm) REVERT: A 589 MET cc_start: 0.8289 (tmm) cc_final: 0.8062 (tmm) REVERT: B 253 LYS cc_start: 0.9180 (tmtt) cc_final: 0.8913 (tptt) REVERT: B 303 LYS cc_start: 0.8414 (ptpp) cc_final: 0.8118 (ptmt) REVERT: B 589 MET cc_start: 0.8255 (tmm) cc_final: 0.7980 (tmm) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.0792 time to fit residues: 26.2842 Evaluate side-chains 184 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.0040 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 256 GLN A 397 GLN B 208 ASN B 397 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.136370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.109689 restraints weight = 24011.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.112527 restraints weight = 12208.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.113926 restraints weight = 7978.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.115291 restraints weight = 6359.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.115738 restraints weight = 5434.197| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11226 Z= 0.144 Angle : 0.677 6.984 15266 Z= 0.343 Chirality : 0.045 0.173 1730 Planarity : 0.005 0.050 1900 Dihedral : 4.700 38.603 1464 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.96 % Allowed : 12.89 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.23), residues: 1350 helix: 1.21 (0.17), residues: 888 sheet: -2.90 (0.73), residues: 46 loop : -3.16 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 330 TYR 0.014 0.002 TYR B 155 PHE 0.019 0.001 PHE A 169 TRP 0.045 0.002 TRP A 348 HIS 0.004 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00326 (11226) covalent geometry : angle 0.67689 (15266) hydrogen bonds : bond 0.03958 ( 682) hydrogen bonds : angle 4.32627 ( 2016) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.6341 (mtt180) cc_final: 0.4922 (mtt90) REVERT: A 260 ASP cc_start: 0.8901 (m-30) cc_final: 0.8627 (m-30) REVERT: A 303 LYS cc_start: 0.8366 (ptpp) cc_final: 0.8108 (pmmt) REVERT: A 448 MET cc_start: 0.7586 (ttm) cc_final: 0.7160 (ttm) REVERT: A 589 MET cc_start: 0.8097 (tmm) cc_final: 0.7750 (tmm) REVERT: B 253 LYS cc_start: 0.9179 (tmtt) cc_final: 0.8863 (tptt) REVERT: B 314 ASN cc_start: 0.9049 (m110) cc_final: 0.8630 (p0) REVERT: B 589 MET cc_start: 0.7956 (tmm) cc_final: 0.7213 (tmm) outliers start: 11 outliers final: 6 residues processed: 219 average time/residue: 0.0790 time to fit residues: 25.8440 Evaluate side-chains 193 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 187 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 94 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 24 optimal weight: 30.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN B 208 ASN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.135088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.107613 restraints weight = 24731.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.110357 restraints weight = 12713.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.111920 restraints weight = 8445.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.113120 restraints weight = 6728.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.113548 restraints weight = 5829.403| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11226 Z= 0.172 Angle : 0.672 6.885 15266 Z= 0.340 Chirality : 0.045 0.188 1730 Planarity : 0.005 0.047 1900 Dihedral : 4.564 39.138 1464 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.79 % Allowed : 16.29 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.24), residues: 1350 helix: 1.36 (0.17), residues: 886 sheet: -3.08 (0.71), residues: 46 loop : -3.08 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 330 TYR 0.013 0.002 TYR B 261 PHE 0.019 0.001 PHE A 169 TRP 0.017 0.002 TRP B 624 HIS 0.003 0.001 HIS A 714 Details of bonding type rmsd covalent geometry : bond 0.00403 (11226) covalent geometry : angle 0.67164 (15266) hydrogen bonds : bond 0.03918 ( 682) hydrogen bonds : angle 4.24538 ( 2016) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.6218 (mtt180) cc_final: 0.4873 (mtt90) REVERT: A 157 MET cc_start: 0.5976 (mpp) cc_final: 0.5666 (mpp) REVERT: A 260 ASP cc_start: 0.8931 (m-30) cc_final: 0.8614 (m-30) REVERT: A 303 LYS cc_start: 0.8436 (ptpp) cc_final: 0.8123 (pmmt) REVERT: A 448 MET cc_start: 0.7616 (ttm) cc_final: 0.7201 (ttm) REVERT: A 589 MET cc_start: 0.8115 (tmm) cc_final: 0.7279 (tmm) REVERT: B 157 MET cc_start: 0.5074 (mpp) cc_final: 0.4770 (mpp) REVERT: B 253 LYS cc_start: 0.9207 (tmtt) cc_final: 0.8937 (tptp) REVERT: B 307 LYS cc_start: 0.9248 (mppt) cc_final: 0.8974 (mtmt) REVERT: B 320 MET cc_start: 0.8692 (mmm) cc_final: 0.8321 (mmm) REVERT: B 589 MET cc_start: 0.7892 (tmm) cc_final: 0.7064 (tmm) outliers start: 32 outliers final: 24 residues processed: 226 average time/residue: 0.0807 time to fit residues: 27.1619 Evaluate side-chains 213 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 256 GLN B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.136414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.110034 restraints weight = 24197.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.112853 restraints weight = 12176.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.114641 restraints weight = 7874.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.115491 restraints weight = 6075.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.116335 restraints weight = 5322.690| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11226 Z= 0.132 Angle : 0.642 6.897 15266 Z= 0.322 Chirality : 0.044 0.310 1730 Planarity : 0.005 0.051 1900 Dihedral : 4.388 38.384 1464 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.53 % Allowed : 18.38 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.24), residues: 1350 helix: 1.51 (0.17), residues: 886 sheet: -3.10 (0.70), residues: 46 loop : -2.92 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 330 TYR 0.014 0.001 TYR B 261 PHE 0.023 0.001 PHE B 72 TRP 0.016 0.001 TRP B 624 HIS 0.002 0.000 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00298 (11226) covalent geometry : angle 0.64250 (15266) hydrogen bonds : bond 0.03615 ( 682) hydrogen bonds : angle 4.14704 ( 2016) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.6252 (mtt180) cc_final: 0.4923 (mtt90) REVERT: A 157 MET cc_start: 0.5931 (mpp) cc_final: 0.5586 (mpp) REVERT: A 260 ASP cc_start: 0.8864 (m-30) cc_final: 0.8604 (m-30) REVERT: A 303 LYS cc_start: 0.8501 (ptpp) cc_final: 0.8239 (pmmt) REVERT: A 448 MET cc_start: 0.7576 (ttm) cc_final: 0.7239 (ttm) REVERT: A 589 MET cc_start: 0.8044 (tmm) cc_final: 0.7197 (tmm) REVERT: B 157 MET cc_start: 0.5232 (mpp) cc_final: 0.4919 (mpp) REVERT: B 253 LYS cc_start: 0.9215 (tmtt) cc_final: 0.8943 (tptp) REVERT: B 263 GLN cc_start: 0.9292 (tp-100) cc_final: 0.8947 (tm-30) REVERT: B 307 LYS cc_start: 0.9242 (mppt) cc_final: 0.8930 (mttp) REVERT: B 320 MET cc_start: 0.8607 (mmm) cc_final: 0.8162 (mmm) REVERT: B 589 MET cc_start: 0.7835 (tmm) cc_final: 0.6788 (tmm) outliers start: 29 outliers final: 18 residues processed: 226 average time/residue: 0.0874 time to fit residues: 29.2824 Evaluate side-chains 211 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.136661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.110343 restraints weight = 24070.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.113064 restraints weight = 12146.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.114658 restraints weight = 7928.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.115892 restraints weight = 6225.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.116314 restraints weight = 5338.542| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11226 Z= 0.131 Angle : 0.640 6.739 15266 Z= 0.319 Chirality : 0.043 0.197 1730 Planarity : 0.005 0.052 1900 Dihedral : 4.304 38.679 1464 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.96 % Allowed : 19.69 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.24), residues: 1350 helix: 1.57 (0.17), residues: 894 sheet: -3.12 (0.69), residues: 46 loop : -2.88 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 330 TYR 0.024 0.001 TYR A 261 PHE 0.017 0.001 PHE B 72 TRP 0.016 0.001 TRP B 348 HIS 0.002 0.000 HIS A 714 Details of bonding type rmsd covalent geometry : bond 0.00298 (11226) covalent geometry : angle 0.63981 (15266) hydrogen bonds : bond 0.03527 ( 682) hydrogen bonds : angle 4.11983 ( 2016) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 157 MET cc_start: 0.5862 (mpp) cc_final: 0.5517 (mpp) REVERT: A 260 ASP cc_start: 0.8889 (m-30) cc_final: 0.8594 (m-30) REVERT: A 448 MET cc_start: 0.7567 (ttm) cc_final: 0.7234 (ttm) REVERT: A 589 MET cc_start: 0.8021 (tmm) cc_final: 0.7154 (tmm) REVERT: A 682 ARG cc_start: 0.8901 (ptt90) cc_final: 0.8668 (ptp90) REVERT: B 157 MET cc_start: 0.5219 (mpp) cc_final: 0.4894 (mpp) REVERT: B 169 PHE cc_start: 0.7661 (m-10) cc_final: 0.7413 (m-80) REVERT: B 253 LYS cc_start: 0.9214 (tmtt) cc_final: 0.8946 (tptp) REVERT: B 263 GLN cc_start: 0.9299 (tp-100) cc_final: 0.8989 (tm-30) REVERT: B 307 LYS cc_start: 0.9244 (mppt) cc_final: 0.8939 (mttp) REVERT: B 536 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7775 (pttt) REVERT: B 589 MET cc_start: 0.7816 (tmm) cc_final: 0.6754 (tmm) outliers start: 34 outliers final: 21 residues processed: 229 average time/residue: 0.0827 time to fit residues: 28.2078 Evaluate side-chains 217 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 641 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 257 ASN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN B 256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.135741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.109633 restraints weight = 24300.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.112330 restraints weight = 12217.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.114098 restraints weight = 7959.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.114874 restraints weight = 6149.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.115550 restraints weight = 5417.248| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11226 Z= 0.143 Angle : 0.648 7.060 15266 Z= 0.323 Chirality : 0.044 0.183 1730 Planarity : 0.005 0.053 1900 Dihedral : 4.270 38.775 1464 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.22 % Allowed : 20.73 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.24), residues: 1350 helix: 1.61 (0.17), residues: 894 sheet: -3.11 (0.68), residues: 46 loop : -2.87 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 330 TYR 0.025 0.001 TYR A 261 PHE 0.017 0.001 PHE A 169 TRP 0.018 0.002 TRP A 348 HIS 0.002 0.001 HIS A 714 Details of bonding type rmsd covalent geometry : bond 0.00330 (11226) covalent geometry : angle 0.64828 (15266) hydrogen bonds : bond 0.03553 ( 682) hydrogen bonds : angle 4.14122 ( 2016) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 157 MET cc_start: 0.5943 (mpp) cc_final: 0.5572 (mpp) REVERT: A 260 ASP cc_start: 0.8846 (m-30) cc_final: 0.8554 (m-30) REVERT: A 448 MET cc_start: 0.7550 (ttm) cc_final: 0.7195 (ttm) REVERT: A 589 MET cc_start: 0.7981 (tmm) cc_final: 0.7373 (tmm) REVERT: A 682 ARG cc_start: 0.8879 (ptt90) cc_final: 0.8572 (ptp90) REVERT: B 157 MET cc_start: 0.5250 (mpp) cc_final: 0.4892 (mpp) REVERT: B 165 MET cc_start: 0.8144 (tpp) cc_final: 0.7821 (tpp) REVERT: B 169 PHE cc_start: 0.7723 (m-10) cc_final: 0.7451 (m-80) REVERT: B 253 LYS cc_start: 0.9253 (tmtt) cc_final: 0.8990 (tptp) REVERT: B 263 GLN cc_start: 0.9311 (tp-100) cc_final: 0.9001 (tm-30) REVERT: B 307 LYS cc_start: 0.9244 (mppt) cc_final: 0.8936 (mttp) REVERT: B 531 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6416 (mt-10) REVERT: B 536 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7814 (pttt) REVERT: B 589 MET cc_start: 0.7821 (tmm) cc_final: 0.6715 (tmm) outliers start: 37 outliers final: 27 residues processed: 227 average time/residue: 0.0834 time to fit residues: 27.9819 Evaluate side-chains 221 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.136561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.110532 restraints weight = 24042.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.113240 restraints weight = 12159.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.114809 restraints weight = 7879.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.115990 restraints weight = 6208.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.116241 restraints weight = 5334.956| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11226 Z= 0.137 Angle : 0.657 9.282 15266 Z= 0.324 Chirality : 0.043 0.209 1730 Planarity : 0.005 0.054 1900 Dihedral : 4.244 38.748 1464 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.70 % Allowed : 21.86 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.24), residues: 1350 helix: 1.56 (0.17), residues: 902 sheet: -3.01 (0.67), residues: 46 loop : -2.96 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 207 TYR 0.026 0.001 TYR A 261 PHE 0.016 0.001 PHE A 169 TRP 0.021 0.002 TRP B 348 HIS 0.002 0.000 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00315 (11226) covalent geometry : angle 0.65673 (15266) hydrogen bonds : bond 0.03529 ( 682) hydrogen bonds : angle 4.14310 ( 2016) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 157 MET cc_start: 0.5876 (mpp) cc_final: 0.5494 (mpp) REVERT: A 260 ASP cc_start: 0.8855 (m-30) cc_final: 0.8552 (m-30) REVERT: A 448 MET cc_start: 0.7628 (ttm) cc_final: 0.7212 (ttm) REVERT: A 589 MET cc_start: 0.7962 (tmm) cc_final: 0.7141 (tmm) REVERT: A 682 ARG cc_start: 0.8850 (ptt90) cc_final: 0.8577 (ptp90) REVERT: B 157 MET cc_start: 0.5106 (mpp) cc_final: 0.4758 (mpp) REVERT: B 253 LYS cc_start: 0.9259 (tmtt) cc_final: 0.8993 (tptp) REVERT: B 263 GLN cc_start: 0.9307 (tp-100) cc_final: 0.9008 (tm-30) REVERT: B 307 LYS cc_start: 0.9253 (mppt) cc_final: 0.8959 (mttp) REVERT: B 511 MET cc_start: 0.6372 (pmm) cc_final: 0.6166 (pmm) REVERT: B 536 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7790 (pttt) REVERT: B 589 MET cc_start: 0.7806 (tmm) cc_final: 0.6772 (tmm) outliers start: 31 outliers final: 26 residues processed: 220 average time/residue: 0.0878 time to fit residues: 28.8988 Evaluate side-chains 224 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 119 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 8 optimal weight: 0.0770 chunk 104 optimal weight: 0.7980 chunk 100 optimal weight: 0.0980 chunk 66 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.139837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.113750 restraints weight = 23892.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.116613 restraints weight = 12058.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.118446 restraints weight = 7801.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.119620 restraints weight = 5987.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.119875 restraints weight = 5113.581| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11226 Z= 0.118 Angle : 0.637 8.489 15266 Z= 0.313 Chirality : 0.043 0.201 1730 Planarity : 0.005 0.055 1900 Dihedral : 4.165 38.789 1464 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.18 % Allowed : 22.82 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.24), residues: 1350 helix: 1.77 (0.18), residues: 890 sheet: -2.92 (0.67), residues: 46 loop : -2.73 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 207 TYR 0.026 0.001 TYR A 261 PHE 0.024 0.001 PHE B 169 TRP 0.025 0.001 TRP B 348 HIS 0.001 0.000 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00254 (11226) covalent geometry : angle 0.63681 (15266) hydrogen bonds : bond 0.03318 ( 682) hydrogen bonds : angle 4.07841 ( 2016) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 157 MET cc_start: 0.5799 (mpp) cc_final: 0.5413 (mpp) REVERT: A 169 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.8037 (t80) REVERT: A 260 ASP cc_start: 0.8842 (m-30) cc_final: 0.8535 (m-30) REVERT: A 266 TYR cc_start: 0.8100 (t80) cc_final: 0.7745 (t80) REVERT: A 448 MET cc_start: 0.7556 (ttm) cc_final: 0.7160 (ttm) REVERT: A 589 MET cc_start: 0.7852 (tmm) cc_final: 0.6960 (tmm) REVERT: A 682 ARG cc_start: 0.8744 (ptt90) cc_final: 0.8539 (ptp90) REVERT: A 689 MET cc_start: 0.8537 (tpt) cc_final: 0.8301 (tpp) REVERT: B 157 MET cc_start: 0.5063 (mpp) cc_final: 0.4711 (mpp) REVERT: B 253 LYS cc_start: 0.9256 (tmtt) cc_final: 0.8988 (tptp) REVERT: B 263 GLN cc_start: 0.9292 (tp-100) cc_final: 0.9025 (tm-30) REVERT: B 307 LYS cc_start: 0.9252 (mppt) cc_final: 0.8955 (mttp) REVERT: B 511 MET cc_start: 0.6197 (pmm) cc_final: 0.5967 (pmm) REVERT: B 589 MET cc_start: 0.7731 (tmm) cc_final: 0.7219 (ttp) outliers start: 25 outliers final: 20 residues processed: 239 average time/residue: 0.0761 time to fit residues: 27.5288 Evaluate side-chains 224 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.137114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.110830 restraints weight = 24152.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.113575 restraints weight = 12298.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.115318 restraints weight = 8030.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.116091 restraints weight = 6236.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.116639 restraints weight = 5506.061| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11226 Z= 0.148 Angle : 0.684 11.835 15266 Z= 0.340 Chirality : 0.044 0.225 1730 Planarity : 0.005 0.056 1900 Dihedral : 4.211 39.127 1464 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.09 % Allowed : 23.87 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.24), residues: 1350 helix: 1.56 (0.17), residues: 912 sheet: -2.95 (0.78), residues: 36 loop : -2.89 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 330 TYR 0.048 0.002 TYR A 469 PHE 0.041 0.001 PHE A 72 TRP 0.028 0.002 TRP A 348 HIS 0.003 0.001 HIS A 542 Details of bonding type rmsd covalent geometry : bond 0.00343 (11226) covalent geometry : angle 0.68395 (15266) hydrogen bonds : bond 0.03558 ( 682) hydrogen bonds : angle 4.12400 ( 2016) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 157 MET cc_start: 0.5896 (mpp) cc_final: 0.5492 (mpp) REVERT: A 169 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.8156 (t80) REVERT: A 260 ASP cc_start: 0.8865 (m-30) cc_final: 0.8574 (m-30) REVERT: A 266 TYR cc_start: 0.8110 (t80) cc_final: 0.7753 (t80) REVERT: A 448 MET cc_start: 0.7611 (ttm) cc_final: 0.7180 (ttm) REVERT: A 511 MET cc_start: 0.6330 (pmm) cc_final: 0.6101 (pmm) REVERT: A 589 MET cc_start: 0.7850 (tmm) cc_final: 0.7644 (ttp) REVERT: A 682 ARG cc_start: 0.8774 (ptt90) cc_final: 0.8569 (ptp90) REVERT: B 157 MET cc_start: 0.5196 (mpp) cc_final: 0.4833 (mpp) REVERT: B 253 LYS cc_start: 0.9267 (tmtt) cc_final: 0.9001 (tptp) REVERT: B 263 GLN cc_start: 0.9302 (tp-100) cc_final: 0.9027 (tm-30) REVERT: B 307 LYS cc_start: 0.9257 (mppt) cc_final: 0.8962 (mttp) REVERT: B 511 MET cc_start: 0.6402 (pmm) cc_final: 0.6166 (pmm) REVERT: B 589 MET cc_start: 0.7858 (tmm) cc_final: 0.7351 (ttp) outliers start: 24 outliers final: 20 residues processed: 225 average time/residue: 0.0854 time to fit residues: 28.4102 Evaluate side-chains 220 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.132540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.106325 restraints weight = 24707.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.109014 restraints weight = 12688.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.110396 restraints weight = 8315.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.111665 restraints weight = 6625.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.112123 restraints weight = 5688.035| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11226 Z= 0.236 Angle : 0.766 10.743 15266 Z= 0.387 Chirality : 0.047 0.251 1730 Planarity : 0.005 0.062 1900 Dihedral : 4.552 39.359 1464 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.26 % Allowed : 24.48 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.23), residues: 1350 helix: 1.15 (0.17), residues: 908 sheet: -2.96 (0.67), residues: 46 loop : -3.09 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 630 TYR 0.031 0.002 TYR A 261 PHE 0.040 0.002 PHE A 72 TRP 0.024 0.002 TRP A 348 HIS 0.005 0.001 HIS A 714 Details of bonding type rmsd covalent geometry : bond 0.00556 (11226) covalent geometry : angle 0.76648 (15266) hydrogen bonds : bond 0.04255 ( 682) hydrogen bonds : angle 4.48836 ( 2016) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.532 Fit side-chains REVERT: A 137 ARG cc_start: 0.6187 (mtt180) cc_final: 0.4811 (mtt90) REVERT: A 157 MET cc_start: 0.5927 (mpp) cc_final: 0.5635 (mpp) REVERT: A 169 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.8068 (t80) REVERT: A 260 ASP cc_start: 0.8919 (m-30) cc_final: 0.8619 (m-30) REVERT: A 266 TYR cc_start: 0.8146 (t80) cc_final: 0.7792 (t80) REVERT: A 448 MET cc_start: 0.7564 (ttm) cc_final: 0.7169 (ttm) REVERT: A 682 ARG cc_start: 0.8880 (ptt90) cc_final: 0.8555 (ptp90) REVERT: B 157 MET cc_start: 0.5376 (mpp) cc_final: 0.4996 (mpp) REVERT: B 253 LYS cc_start: 0.9272 (tmtt) cc_final: 0.9002 (tptp) REVERT: B 511 MET cc_start: 0.6096 (pmm) cc_final: 0.5866 (pmm) REVERT: B 589 MET cc_start: 0.8123 (tmm) cc_final: 0.7601 (ttp) outliers start: 26 outliers final: 22 residues processed: 214 average time/residue: 0.0955 time to fit residues: 30.4891 Evaluate side-chains 219 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 56 optimal weight: 0.9980 chunk 93 optimal weight: 40.0000 chunk 67 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN B 208 ASN ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.136819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.110669 restraints weight = 24104.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.113490 restraints weight = 12190.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.115143 restraints weight = 7901.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.116368 restraints weight = 6153.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116802 restraints weight = 5265.187| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11226 Z= 0.137 Angle : 0.698 11.339 15266 Z= 0.345 Chirality : 0.044 0.216 1730 Planarity : 0.005 0.063 1900 Dihedral : 4.376 38.743 1464 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.00 % Allowed : 24.65 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.24), residues: 1350 helix: 1.43 (0.17), residues: 904 sheet: -2.85 (0.68), residues: 46 loop : -2.95 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 630 TYR 0.033 0.002 TYR A 469 PHE 0.039 0.001 PHE A 72 TRP 0.031 0.002 TRP A 348 HIS 0.003 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00313 (11226) covalent geometry : angle 0.69779 (15266) hydrogen bonds : bond 0.03666 ( 682) hydrogen bonds : angle 4.24362 ( 2016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1579.13 seconds wall clock time: 28 minutes 7.27 seconds (1687.27 seconds total)